William Shawcross, the Old Etonian head of the Charity Commission, has been accused of hypocrisy over his attacks on high executive pay among development charities after it emerged that Britain's public schools pay some of the biggest salaries in the charitable sector.

It has emerged that the salaries paid to staff working within some independent schools, which also have tax-exempt charitable status, dwarf the remuneration packages at development charities.

Accounts for Eton College, where Shawcross was educated, show that it pays 40 staff more than £100,000 a year, including seven between £120,000 and £129,000, and its head between £230,000 and £239,000, although all the charity accounts figures include pension and national insurance contributions. The bursar for Eton said that its head, Tony Little, has a basic salary of £179,375.

An analysis of the accounts of other independent schools shows that at Harrow school seven members of staff earn more than £100,000, including one who earns between £190,001 and £200,000.

At Westminster School, the alma mater of deputy prime minister Nick Clegg, 41 members of staff earn more than £60,000 and one is on £140,150. At St Paul's school, three members of staff have a payment package worth more than £100,000 and one earns between £200,000 and £209,000.

Sir Stephen Bubb, head of the Association of Chief Executives of Voluntary Organisations (Acevo), said he believed that Shawcross had specifically targeted his criticism at development charities, a claim denied by the commission, and that he was feeding into a political agenda.

He said: "It is curious that the chair of the Charity Commission singled out international development charities over pay. If charities like the great universities and top public schools believe they need to pay good salaries to attract the best talent, then why does the same principle not apply to the aid charities, albeit their pay is more modest.

"Mr Shawcross, by choosing to target his comments in this way, risks aligning the Charity Commission with a political campaign on foreign aid. That is what will bring the charity world into disrepute rather than what aid charities pay to recruit the best leaders."

A commission spokesman said that Shawcross had responded generally in regard to charity salaries and had not meant to be specific about development charities, although the initial report on which he had commented had concerned them. She said: "The comment made by William Shawcross was a general comment about charities. He did make it clear that it is not for the commission to tell charities how much they should pay their executives. That is a matter for their trustees.

"Following the media coverage last week, the National Council of Voluntary Organisations on Monday announced they were intending to work on an advisory code for charity trustees when setting senior staff salaries, and we have welcomed this initiative and said we are happy to be involved in a process that supports trustees to fulfil their duties when making decisions."